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matcher - Waterman-Eggert local alignment of two sequences


matcher -asequence sequence -bsequence sequence [-datafile matrix] [-alternatives integer]
[-gapopen integer] [-gapextend integer] -outfile align

matcher -help


matcher is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Alignment:Local" command group(s).


Input section
-asequence sequence

-bsequence sequence

-datafile matrix
This is the scoring matrix file used when comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of the EMBOSS installation.

Additional section
-alternatives integer
This sets the number of alternative matches output. By default only the highest
scoring alignment is shown. A value of 2 gives you other reasonable alignments. In
some cases, for example multidomain proteins of cDNA and genomic DNA comparisons,
there may be other interesting and significant alignments. Default value: 1

-gapopen integer
The gap penalty is the score taken away when a gap is created. The best value depends
on the choice of comparison matrix. The default value of 14 assumes you are using the
EBLOSUM62 matrix for protein sequences, or a value of 16 and the EDNAFULL matrix for
nucleotide sequences. Default value: @($(acdprotein)? 14 : 16)

-gapextend integer
The gap length, or gap extension, penalty is added to the standard gap penalty for
each base or residue in the gap. This is how long gaps are penalized. Usually you will
expect a few long gaps rather than many short gaps, so the gap extension penalty
should be lower than the gap penalty. An exception is where one or both sequences are
single reads with possible sequencing errors in which case you would expect many
single base gaps. You can get this result by setting the gap penalty to zero (or very
low) and using the gap extension penalty to control gap scoring. Default value:
@($(acdprotein)? 4 : 4)

Output section
-outfile align

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